About Egghead

Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

Astronomers using NASA’s Hubble Space Telescope have for the first time spotted four images of the same distant exploding star, arranged in an “Einstein’s Cross,” a cross-shape pattern created by the powerful gravity of a foreground galaxy embedded in a massive cluster of galaxies.

Distant supernova split into four images by massive galaxy cluster in the four ground. Because light is taking different paths through the cluster, other images of the supernova may appear later.

First predicted by Albert Einstein, gravitational lensing is similar to a glass lens bending light to magnify and distort the image of an object behind it.

Although astronomers have discovered dozens of multiply imaged galaxies and quasars, they have never seen a stellar explosion resolved into several images.

The lensed supernova was found by the Grism Lens Amplified Survey from Space (GLASS) collaboration. The GLASS group is working with the FrontierSN team to analyze the supernova. A paper describing the discovery appeared March 6 in a special issue of the journal Science celebrating the centenary of Albert Einstein’s Theory of General Relativity.

“Until now, we’ve only been able to study galaxies that are multiply lensed,” said Marusa Bradac, an astronomer in the UC Davis Department of Physics and coauthor on the paper. “For the first time we now see a supernova in this role and this is extremely exciting.”

This unique observation will help astronomers refine their estimates of the amount and distribution of dark matter in the lensing galaxy and cluster. Dark matter cannot be seen directly but is believed to make up most of the universe’s mass.

“These kinds of systems are pure gold, because they allow us to study the supernova and the dark matter in the galaxy, as well as determine the history of the entire Universe,” Bradac said.

A supernova is a short-lived event, but when the four images fade away astronomers will have a rare chance to catch a rerun because the current four-image pattern is only one component of the lensing display. The clumps of dark matter in the galaxy cluster are bending images of the supernova through multiple different routes, like train tracks through a mountain range. The supernova may have appeared in a single image some 20 years ago, and it is expected to reappear once more in the next one to five years.

The prediction of a future appearance is based on computer models of the cluster, which describe the various paths the divided light is taking through the maze of clumpy dark matter in the galactic grouping. The supernova images do not arrive at Earth at the same time because some of the light is delayed as it travels around bends created by the gravity of dense dark matter in the intervening galaxy cluster.

“Our model for the dark matter in the cluster gives us the prediction of when the next image will appear because it tells us how long each train track is, which correlates with time,” said Steve Rodney of Johns Hopkins University, leader of the FrontierSN team. “We already missed one that we think appeared about 20 years ago, and we found these four images after they had already appeared. The prediction of this future image is the one that is most exciting because we might be able to catch it. We hope to come back to this field with Hubble, and we’ll keep looking to see when that expected next image appears.”

Measuring the time delays between images will help the astronomers fine-tune the models that map out the cluster’s mass.

Patrick Kelly of UC Berkeley spotted the four images of the exploding star on Nov. 11, 2014, in the galaxy cluster MACS J1149.6+2223, located more than 5 billion light-years away. The FrontierSN and GLASS teams teams spent a week analyzing the object’s light, confirming it was the signature of a supernova. They then turned to the W. M. Keck Observatory on Mauna Kea, in Hawaii, to measure the distance to the supernova’s host galaxy, which is 9.3 billion light-years from Earth.

The supernova appears about 20 times brighter than its natural brightness, because it is being magnified by both the lens of the galaxy cluster and by a massive elliptical galaxy within the cluster.

The astronomers nicknamed the supernova Refsdal in honor of Norwegian astronomer Sjur Refsdal, who, in 1964, first proposed using time-delayed images from a lensed supernova to study the expansion of the universe.

Cicadas in the genus Karenia lack the specialized sound-producing structures, called tymbals, that characterize most cicadas, according to Nansen and colleagues Changquing Luo and Cong Wei, both of Northwest A & F University, Shaanxi, China.

But the word mute is misleading, says Nansen. “They do indeed produce sounds.”

The researchers found that Karenia caelatata produces impact sounds by banging the leading edge, or costa of the forewing against the operculum, a lid covering the insect’s equivalent of an ear. The operculum of K. caelatata is larger than in other cicadas and extends past the edge of the body.

When the male mute cicadas are at rest, the wings are held back over the body with the trailing edge of the wing is locked into a groove on the animals back. When the male wants to make some noise, he lifts his abdomen from the tree branch and rapidly opens and closes his wings. With the back edge of the wing locked in place, the leading edge beats against the hard operculum to make a clicking sound. It’s somewhat like beating a drum while other cicada species with tymbal mechanisms play an orchestra of diverse and loud sounds.

“The new sound-production mechanism expands our knowledge on the diversity of acoustic signaling behavior in cicadas and further underscores the need for more bioacoustic studies on cicadas which lack tymbal mechanism,” Nansen and colleagues concluded in their abstract.

Video: How the mute cicada sings (ScienceNews)

Cicadas, also known as “tree crickets” (from Latin cicada), are among the most widely recognized of insects due to their large size, usually 2 to 5 centimeters or more, and loud sounds, sometime as high as 120 decibels. Theirs is among the loudest of all insect-produced sounds. Cicadas live in warm climates, from temperate to tropical. Immature cicadas spend most of their lives sucking juice from tree roots. The adults suck plant juices from stems.

The best-known North American genus, Magicicada, has a long life cycle of 13 or 17 years and emerges in great numbers.

Cicadas damage cultivated crops, shrubs, and trees, mainly from females scarring tree branches where they lay their eggs. In many cultures, cicadas are a delicacy on the menu.

Recreating the violent conditions of Earth’s formation, scientists are learning more about how iron vaporizes and how this iron rain affected the formation of the Earth and Moon. The study is published March 2 in Nature Geoscience.

“We care about when iron vaporizes because it is critical to learning how Earth’s core grew,” said co-author Sarah Stewart, UC Davis professor of Earth and Planetary Sciences.

Shock and release

Scientists from Lawrence Livermore National Laboratory, Sandia National Laboratory, Harvard University and UC Davis used one of the world’s most powerful radiation sources, the Sandia National Laboratories Z-machine, to recreate conditions that led to Earth’s formation. They subjected iron samples to high shock pressures in the machine, slamming aluminum plates into iron samples at extremely high speeds. They developed a new shock-wave technique to determine the critical impact conditions needed to vaporize the iron.

The Z Machine at Sandia Lab is one of the most powerful radiation sources in the nation.

The researchers found that the shock pressure required to vaporize iron is much lower than expected, which means more iron was vaporized during Earth’s formation than previously thought.

Iron rain

Lead author Richard Kraus, formerly a graduate student under Stewart at Harvard, is now a research scientist at Lawrence Livermore National Laboratory. He said the results may shift how planetary scientists think about the processes and timing of Earth’s core formation.

“Rather than the iron in the colliding objects sinking down directly to the Earth’s growing core, the iron is vaporized and spread over the surface within a vapor plume,” said Kraus. “This means that the iron can mix much more easily with Earth’s mantle.”

After cooling, the vapor would have condensed into an iron rain that mixed into the Earth’s still-molten mantle.

To the moon

This process may also explain why the Moon, which is thought to have formed by this time, lacks iron-rich material despite being exposed to similarly violent collisions. The authors suggest the Moon’s reduced gravity could have prevented it from retaining most of the vaporized iron.

The work was conducted under the Sandia Z Fundamental Science Program and supported by the U.S. Department of Energy National Nuclear Security Administration.

Scientists and breeders working with poultry and livestock species will get a new set of tools from an international project that includes the University of California, Davis.

The UC Davis team is led by functional genomicist Huaijun Zhou, an associate professor and Chancellor’s Fellow in the Department of Animal Science. The researchers will focus on the genomes of the chicken, cow and pig, which make up the largest meat-producing industries in the United States.

“Initial sequences of the chicken, bovine and swine genomes were published during the last decade, identifying the genes that actually translate genetic material into proteins,” Zhou said.

“Those sequences represent the beginning of an exciting path to understanding the underlying digital code for the biology of these important agricultural species,” he said. “But it has become increasingly apparent that we also need to determine the function of surrounding regions of the genes in the genome, sometimes referred to as ‘functional elements.’ ”

Functional elements

These functional elements – once thought to be “junk DNA” because they don’t encode proteins – are now known to play a critical role in regulating how genes are expressed and how the genetic material is manifested in an animal’s traits.

“The functional elements and the molecular processes they influence, are key to controlling development and complex traits such as production, immune response, reproduction and behavior,” Zhou said.

Information gleaned by the new effort will aid breeders in developing healthier and more productive and sustainable farm animals.

Other collaborators are Hans Cheng, a research geneticist at the USDA-ARS Avian Disease and Oncology Laboratory at Michigan State University; Chris Tuggle, an animal scientist at Iowa State University; Cathy Ernst, an animal scientist at Michigan State University; Vicki Leesburg an agricultural statistician with the USDA-ARS; Bing Ren, a molecular geneticist at the Institute of Genomics Institute, UC San Diego; Jim Kent, a bioinformatist at the UCSC Genome Browser; and Paul Flicek, a research scientist at EMBL-EBI.

The UC Davis project is provided by a $500,000 grant from the U.S. Department of Agriculture – National Institute of Food and Agriculture, and is also supported by the U.S. Poultry, Cattle, and Swine Genomes Coordination Funds; the National Pork Board; and Aviagen LTD.

A hexane (six-carbon) molecule between two gold electrodes. A new UC Davis technique gives better measurements of these circuits. (Josh Hihath/UC Davis)

It’s nearly 50 years since Gordon Moore predicted that the density of transistors on an integrated circuit would double every two years. “Moore’s Law” has turned out to be a self-fulfilling prophecy that technologists pushed to meet, but to continue into the future, engineers will have to make radical changes to the structure or composition of circuits. One potential way to achieve this is to develop devices based on single-molecule connections.

New work by Josh Hihath’s group at the UC Davis Department of Electrical and Computer Engineering, published Feb. 16 in the journal Nature Materials, could help technologists make that jump. Hihath’s laboratory has developed a method to measure the conformation of single molecule “wiring,” resolving a clash between theoretical predictions and experiments.

“We’re trying to make transistors and diodes out of single molecules, and unfortunately you can’t currently control exactly how the molecule contacts the electrode or what the exact configuration is,” Hihath said. “This new technique gives us a better measurement of the configuration, which will provide important information for theoretical modeling.”

Until now, there has been a wide gap between the predicted electrical behavior of single molecules and experimental measurements, with results being off by as much as ten-fold, Hihath said.

Hihath’s experiment uses a layer of alkanes (short chains of carbon atoms, such as hexane, octane or decane) with either sulfur or nitrogen atoms on each end that allow them to bind to a gold substrate that acts as one electrode. The researchers then bring the gold tip of a Scanning Tunneling Microscope towards the surface to form a connection with the molecules. As the tip is then pulled away, the connection will eventually consist of a single-molecule junction that contains six to ten carbon atoms (depending on the molecule studied at the time).

By vibrating the tip of the STM while measuring electrical current across the junction, Hihath and colleagues were able to extract information about the configuration of the molecules.

“This technique gives us information about both the electrical and mechanical properties of the system and tells us what the most probable configuration is, something that was not possible before,” Hihath said.

The researchers hope the technique can be used to make better predictions of how molecule-scale circuits behave and design better experiments.

Coauthors on the paper are graduate students Habid Rascón-Ramos and Yuanhui Li and postdoctoral researcher Juan Manuel Artés, all at UC Davis. The work was supported by the National Science Foundation and the RISE program of the UC Davis Office of Research.

The morning session included a keynote address by Prof. Elizabeth Blackburn of UCSF and a panel discussion on “Scientific discovery and innovation: What can the future look like at the nexus of food, agriculture and health?”

The afternoon included a presentation on the African Orphan Crops Consortium by Howard Yana Shapiro and Allen Van Deynze, and panel discussions on solving agriculture’s greatest challenges and the role of venture capital in innovation.

Efforts to bring populations of endangered white abalone back from the brink of extinction through captive breeding appear to be working, according to scientists at the UC Davis Bodega Marine Laboratory.

In 2012, UC Davis researchers achieved the first successful captive spawning of the endangered white abalone in nearly a decade. The breeding program had about 70 abalone then. After four more successful spawning events in 2013 and 2014, there are now a few thousand animals in captivity through the program. The scientists are hopeful for even greater numbers as they gear up for another spawning season this spring.

8-month old white abalone in the laboratory (Bodega Marine Lab)

“We now have enough abalone in the program where we can start thinking about testing strategies to put some back into the ocean,” said Kristin Aquilino, a postdoctoral scholar at Bodega Marine Laboratory. “We’re not where we need to be for large-scale outplanting yet. To really save the species, we’re going to need to produce even more animals each year, but we’re excited about this increase.”

The scientists credit the successful spawning to a few tweaks in their process. Over time, they have incorporated more animals into each spawning attempt, which increases the chances of getting both males and females to spawn. More sophisticated facilities also allow scientists to better control the diet of young abalone at key times of their development. For example, natural fatality rates can climb above 90 percent when abalone transition from the swimming larval stage into crawling snails. Increasing their survival even by 1 percent can mean a difference of thousands of animals.

If breeding white abalone is so difficult in a controlled environment, what chance might they have in the wild, open ocean? It helps to remember that the decline of white abalone was due to overfishing, and not habitat destruction.

“If they were successfully reproducing without us before we fished them all away, hopefully whatever they need is still out there,” Aquilino said. “Their habitat is still great, so maybe captive-bred animals can thrive in the wild even better than in the lab. But their population needs a kickstart.”

UC Davis is working with partners in southern California, including UC Santa Barbara, Aquarium of the Pacific, Cabrillo Marine Aquarium, and the Santa Barbara Museum of Natural History Sea Center to breed captive white abalone. Efforts are funded by the National Oceanic and Atmospheric Administration.

Nature has many examples of self-assembly, and bioengineers are interested in copying or manipulating these systems to create useful new materials or devices. Amyloid proteins, for example, can self-assemble into the tangled plaques associated with Alzheimer’s disease — but similar proteins can also form very useful materials, such as spider silk, or biofilms around living cells. Researchers at UC Davis and Rice University have now come up with methods to manipulate natural proteins so that they self-assemble into amyloid fibrils. The paper is published online by the journal ACS Nano.

“These are big proteins with lots of flat surfaces suitable for functionalization, for example to grow photovoltaics or to attach to other surfaces,” said Dan Cox, a physics professor at UC Davis and coauthor on the paper. They could be used as “scaffolding” for tissue engineering, and potentially could be programmed so that other particles or proteins could be attached in specific locations or arrays. Amyloids are also tough: they can withstand boiling, attack by digestive proteins and ultraviolet radiation.

Maria Peralta, a graduate student in chemistry at UC Davis, and colleagues made the amyloid fibrils by tweaking natural “antifreeze” proteins from ryegrass and an insect, spruce budworm. These proteins allow some plants and animals to withstand very cold temperatures by preventing the growth of ice crystals, but they do not naturally self-assemble into larger structures.

Making spruce budworm antifreeze protein into amyloid fibrils. The cap structure (red) was removed and other structures adjusted so that molecules could link up as fibrils (bottom).

The researchers removed cap structures from the end of the antifreeze proteins. They were then able to let them self-assemble into fibrils with predictable heights, a potential new material for bioengineering.

The article by researchers at UC Davis, Arizona State University, Georgia State University and Yale University provides evidence that the novel A/H1N1 influenza outbreak that hit Mexico City in April 2009 could have been worse, but spread of the virus was reduced by people’s behavioral response of distancing themselves from each other.

In April 2009 the Mexican federal government closed public schools in Mexico City and ‘social distancing’ measures were put in place. The researchers used home television viewing in Central Mexico as an indicator of behavioral response during the 2009 A/H1N1 pandemic.

Television ratings data are consistently and widely available and “highly correlated with time spent in the home,” said UC Davis economist Michael Springborn, lead author of the study. These data provide a good indicator for the level of social interaction, because time spent watching television generally increases with time spent at home. And when people are home, they are limiting the number of contacts they make.

“We found that the behavioral response to the outbreak was initially strong but waned sooner than expected,” said Springborn. This dynamic is interpreted as a “rebound effect”. At the onset of a flu outbreak, the public responds strongly to the directed control policies. But over time, there was evidence that people began to spend less time in the confines of their homes. This happened even through the true risk had not fully waned.

“This suggests that efforts to utilize social distancing to mitigate disease spread may have a limited window of efficacy, i.e. before pent up-demand for activities outside the home takes precedence,” Springborn said.

There is historical evidence for this behavior. Observations from the 1918 influenza pandemic in Australia showed that when the perceived risk decreased the public reverted back to normal behavior.

Certain age groups and socio-economic groups responded more strongly than others. The researchers found that the increase in TV watching was more pronounced for children and wealthier groups. The authors speculate that those from poorer backgrounds may face greater difficulty in taking self-protective actions like social distancing, for example due to less flexibility with working hours. These differences between demographic groups could have public health policy implications for directing outbreak response assistance to those with lower financial means or increasing access to paid sick-leave for low-wage workers.

The findings also provide insight for selection of the duration and strength of major interventions (closing of businesses and cancelling public events) versus other forms of assistance, such as distributing masks.

The study drew on the combined disciplinary strengths of epidemiology and economics to create a new model that incorporates behavioral responses into existing models of disease spread.

Social distancing policies may be effective against pandemic influenza. However, people don’t need to wait. It is important to remember that other behaviors, such as washing hands and wearing facemasks, could contribute and should be routine in order to reduce transmission.

While many Americans were enjoying a holiday weekend, biomedical engineering students at UC Davis worked straight through Saturday and Sunday, Jan. 17-18, to design and prototype a medical device…for bats. The effort was the first “Make-a-thon” organized by the UC Davis Biomedical Engineering Society.

“It’s the design process on steroids,” said Anthony Passerini, associate professor of biomedical engineering and director of the department’s senior design program. “The teams were doing over two days what they normally do over two quarters. They were highly constrained by time, materials, and manufacturing techniques. It was a great learning experience and a lot of fun for everyone.”

Over the weekend, teams of students worked on a device to take skin biopsies from wild bats to aid research into White-nose syndrome. Caused by the fungus Pseudogymnoascus destructans, White-nose syndrome is a recently recognized killer of hibernating bats that is spreading rapidly across North America, wiping out up to 90 percent of some bat colonies and up to 80 percent of the entire population of bats that hibernate in caves in the northeastern U.S.

Bats matter: they are among the most important consumers of insects that plague agricultural crops. The economic losses due to the reduction in insect suppression are estimated to be anywhere from $4 to $50 billion.

UC Davis veterinary pathologist Kevin Keel and Barbara Shock, a wildlife disease ecologist at the UC Davis School of Veterinary Medicine, first approached TEAM Facilities manager Steven Lucero to develop a skin biopsy tool for wild bats, which became the focus of the Make-a-thon.

“Our research is an attempt to find ways to mitigate the mortality of bats in affected caves. Using tissue explants as a model of infection is a powerful tool that enables us to mimic the infection on bats to better understand how we might be able to limit its growth on the skin. Any tool that makes this more efficient could help us find better ways to help bats,” Keel said.

The sixty participants of the Make-a-thon were asked to design a single tool that would minimize handling of the bat, while being highly portable and easy for one person to use. The tool needs to cut the tiny piece of skin while adhering it to a support so that it is stretched for histological purposes. A single field tool that can be used by one person and does not require a cutting board will be both simpler for biologists and faster and easier for bats.

Faculty and industry judges evaluated each design and advanced four of the most feasible projects, two from UC Davis and two from the University of Southern California (USC), to the prototyping phase of the competition. These projects were assisted by the UC Davis TEAM Facility in producing working prototypes of their designs.

After testing the designs, the team of Aaron Kho, E. Aaron Cohen, Lucas Murray, Natalya A. Shelby and Shonit Sharma of UC Davis were declared Overall Winners. Their device was inspired by a piercing gun. When tested, the prototype successfully cut through a bat wing in the laboratory. Awards for “Most Potential” and “Most Creative” went to teams from UC Davis and San Jose State University, respectively.

“It was truly remarkable seeing the diversity of designs,” said Assistant Professor Jennifer Choi, one of the faculty judges for the event. “When I spoke to the participants, they were all very excited in being able to play a significant role in further understanding this critical syndrome.”

Hands-on experiences like these are critical in inspiring students to learn, said Jerry C. Hu, assistant director of the TEAM Facilities.

“We had one team consisting only of freshmen and sophomores who learned to CAD overnight! The Make-a-thon is illustrative of TEAM’s mission to benefit education, research, and the community at large. We are excited to start manufacturing the winning prototype for researchers to use across the US before the bats come out of hibernation,” Hu said.